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<li class="navelem"><a class="el" href="dir_3dc1dabd28ba78e072d14d3fcfc90454.html">SPHINXsys</a></li><li class="navelem"><a class="el" href="dir_48ea983704c43b6d88c1fa3f4d09e369.html">src</a></li><li class="navelem"><a class="el" href="dir_0a0d9ef1793521534f0094f317758287.html">shared</a></li><li class="navelem"><a class="el" href="dir_536e372c8df10cac250269553cb892e1.html">materials</a></li>  </ul>
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<div class="title">diffusion_reaction.h</div>  </div>
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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">/* -------------------------------------------------------------------------*</span></div><div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">*                               SPHinXsys                                   *</span></div><div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">* --------------------------------------------------------------------------*</span></div><div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">* SPHinXsys (pronunciation: s&#39;finksis) is an acronym from Smoothed Particle *</span></div><div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">* Hydrodynamics for industrial compleX systems. It provides C++ APIs for    *</span></div><div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">* physical accurate simulation and aims to model coupled industrial dynamic *</span></div><div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">* systems including fluid, solid, multi-body dynamics and beyond with SPH   *</span></div><div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">* (smoothed particle hydrodynamics), a meshless computational method using  *</span></div><div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">* particle discretization.                                                  *</span></div><div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment">*                                                                           *</span></div><div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment">* SPHinXsys is partially funded by German Research Foundation               *</span></div><div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">* (Deutsche Forschungsgemeinschaft) DFG HU1527/6-1, HU1527/10-1             *</span></div><div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">* and HU1527/12-1.                                                          *</span></div><div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">*                                                                           *</span></div><div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment">* Portions copyright (c) 2017-2020 Technical University of Munich and       *</span></div><div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="comment">* the authors&#39; affiliations.                                                *</span></div><div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">*                                                                           *</span></div><div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">* Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may   *</span></div><div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">* not use this file except in compliance with the License. You may obtain a *</span></div><div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment">* copy of the License at http://www.apache.org/licenses/LICENSE-2.0.        *</span></div><div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment">*                                                                           *</span></div><div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment">* --------------------------------------------------------------------------*/</span></div><div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="preprocessor">#pragma once</span></div><div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div><div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="base__material_8h.html">base_material.h</a>&quot;</span></div><div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="solid__particles_8h.html">solid_particles.h</a>&quot;</span></div><div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor">#include &lt;map&gt;</span></div><div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &lt;functional&gt;</span></div><div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="keyword">using namespace </span><a class="code" href="namespacestd_1_1placeholders.html">std::placeholders</a>;</div><div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;</div><div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="keyword">namespace </span><a class="code" href="namespace_s_p_h.html">SPH</a> </div><div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;{</div><div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00045"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html">   45</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html">DiffusionReactionParticles</a>;</div><div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_electro_physiology_particles.html">ElectroPhysiologyParticles</a>;</div><div class="line"><a name="l00051"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_base_diffusion.html">   51</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_base_diffusion.html">BaseDiffusion</a></div><div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;    {</div><div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00055"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_base_diffusion.html#ad28fcfc65a19319a7ee1480e4e5ba9a6">   55</a></span>&#160;        <a class="code" href="class_s_p_h_1_1_base_diffusion.html#ad28fcfc65a19319a7ee1480e4e5ba9a6">BaseDiffusion</a>(<span class="keywordtype">size_t</span> diffusion_species_index, <span class="keywordtype">size_t</span> gradient_species_index)</div><div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;        : diffusion_species_index_(diffusion_species_index), gradient_species_index_(gradient_species_index) {};</div><div class="line"><a name="l00057"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_base_diffusion.html#a1cf2a7e873e1bf1c0666793b5ebff900">   57</a></span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_base_diffusion.html">BaseDiffusion</a>() {};</div><div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;</div><div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;        <span class="keywordtype">size_t</span> diffusion_species_index_;</div><div class="line"><a name="l00062"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_base_diffusion.html#a1b83eb4cf023bf6fc5249f51b856494b">   62</a></span>&#160;        <span class="keywordtype">size_t</span> <a class="code" href="class_s_p_h_1_1_base_diffusion.html#a1b83eb4cf023bf6fc5249f51b856494b">gradient_species_index_</a>;</div><div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;</div><div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;        <span class="keyword">virtual</span> Real getReferenceDiffusivity() = 0;</div><div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;        <span class="keyword">virtual</span> Real getInterParticleDiffusionCoff(<span class="keywordtype">size_t</span> particle_i, <span class="keywordtype">size_t</span> particle_j, Vecd&amp; direction_from_j_to_i) = 0;</div><div class="line"><a name="l00069"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_base_diffusion.html#ad0641c7cb654e35b59e3ffc15472b9a1">   69</a></span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_base_diffusion.html#ad0641c7cb654e35b59e3ffc15472b9a1">initializeLocalDiffusionProperties</a>(<a class="code" href="class_s_p_h_1_1_base_particles.html">BaseParticles</a>* base_particles) {};</div><div class="line"><a name="l00071"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_base_diffusion.html#a4d54baaebbd670cd125cfc2874a2b6ff">   71</a></span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_base_diffusion.html#a4d54baaebbd670cd125cfc2874a2b6ff">setupLocalDiffusionProperties</a>(StdVec&lt;Vecd&gt;&amp; material_fiber) {};</div><div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;    };</div><div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;</div><div class="line"><a name="l00078"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_isotropic_diffusion.html">   78</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_isotropic_diffusion.html">IsotropicDiffusion</a> : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_base_diffusion.html">BaseDiffusion</a></div><div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;    {</div><div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;        Real diff_cf_; <span class="comment">/*&gt; diffusion coefficient. */</span></div><div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;</div><div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00085"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_isotropic_diffusion.html#a747fa5685c40065bf66e758301ffe5de">   85</a></span>&#160;        <a class="code" href="class_s_p_h_1_1_isotropic_diffusion.html#a747fa5685c40065bf66e758301ffe5de">IsotropicDiffusion</a>(<span class="keywordtype">size_t</span> diffusion_species_index, <span class="keywordtype">size_t</span> gradient_species_index,</div><div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;            Real diff_cf = 1.0) : <a class="code" href="class_s_p_h_1_1_base_diffusion.html">BaseDiffusion</a>(diffusion_species_index, gradient_species_index),</div><div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;            diff_cf_(diff_cf) {};</div><div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_isotropic_diffusion.html">IsotropicDiffusion</a>() {};</div><div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;</div><div class="line"><a name="l00091"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_isotropic_diffusion.html#a8778717ace62181005a763fed4ce3f8c">   91</a></span>&#160;        <span class="keyword">virtual</span> Real <a class="code" href="class_s_p_h_1_1_isotropic_diffusion.html#a8778717ace62181005a763fed4ce3f8c">getReferenceDiffusivity</a>()<span class="keyword"> override </span>{ <span class="keywordflow">return</span> diff_cf_; };</div><div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_isotropic_diffusion.html#aac18dd1f017b84629c0f283f91aeaa3d">   93</a></span>&#160;        <span class="keyword">virtual</span> Real <a class="code" href="class_s_p_h_1_1_isotropic_diffusion.html#aac18dd1f017b84629c0f283f91aeaa3d">getInterParticleDiffusionCoff</a>(<span class="keywordtype">size_t</span> particle_i, <span class="keywordtype">size_t</span> particle_j, Vecd&amp; direction_from_j_to_i)<span class="keyword"> override</span></div><div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;<span class="keyword">        </span>{</div><div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;            <span class="keywordflow">return</span> diff_cf_;</div><div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;        };</div><div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;    };</div><div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;</div><div class="line"><a name="l00103"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_directional_diffusion.html">  103</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_directional_diffusion.html">DirectionalDiffusion</a> : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_isotropic_diffusion.html">IsotropicDiffusion</a></div><div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;    {</div><div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;        Vecd bias_direction_; <span class="comment">/*&gt; Reference bias direction. */</span></div><div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;        <span class="comment">/*&gt; The bias diffusion coefficient along the fiber direction. */</span></div><div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;        Real bias_diff_cf_;</div><div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;        <span class="comment">/*&gt; The transformed diffusivity with inverse Cholesky decomposition. */</span></div><div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;        Matd transf_diffusivity_;</div><div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;        <span class="keywordtype">void</span> initializeDirectionalDiffusivity(Real diff_cf, Real bias_diff_cf, Vecd bias_direction);</div><div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00115"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_directional_diffusion.html#ac02518b789d53ccf663d037b16a1a0d5">  115</a></span>&#160;        <a class="code" href="class_s_p_h_1_1_directional_diffusion.html#ac02518b789d53ccf663d037b16a1a0d5">DirectionalDiffusion</a>(<span class="keywordtype">size_t</span> diffusion_species_index, <span class="keywordtype">size_t</span> gradient_species_index,</div><div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;            Real diff_cf, Real bias_diff_cf, Vecd bias_direction) </div><div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;            : <a class="code" href="class_s_p_h_1_1_isotropic_diffusion.html">IsotropicDiffusion</a>(diffusion_species_index, gradient_species_index,</div><div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;                diff_cf), bias_diff_cf_(bias_diff_cf), bias_direction_(bias_direction),</div><div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;            transf_diffusivity_(1.0) </div><div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;        {</div><div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;            initializeDirectionalDiffusivity(diff_cf, bias_diff_cf, bias_direction);</div><div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;        };</div><div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_directional_diffusion.html">DirectionalDiffusion</a>() {};</div><div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;</div><div class="line"><a name="l00126"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_directional_diffusion.html#a105351f84960ad51e5d47cf3a1ddb2e4">  126</a></span>&#160;        <span class="keyword">virtual</span> Real <a class="code" href="class_s_p_h_1_1_directional_diffusion.html#a105351f84960ad51e5d47cf3a1ddb2e4">getReferenceDiffusivity</a>()<span class="keyword"> override</span></div><div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;<span class="keyword">        </span>{</div><div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;            <span class="keywordflow">return</span> SMAX(diff_cf_, diff_cf_ + bias_diff_cf_);</div><div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;        };</div><div class="line"><a name="l00136"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_directional_diffusion.html#a9cddff8508ce415c43e169d522e3e1d8">  136</a></span>&#160;        <span class="keyword">virtual</span> Real <a class="code" href="class_s_p_h_1_1_directional_diffusion.html#a9cddff8508ce415c43e169d522e3e1d8">getInterParticleDiffusionCoff</a>(<span class="keywordtype">size_t</span> particle_index_i, <span class="keywordtype">size_t</span> particle_index_j, Vecd&amp; inter_particle_direction)<span class="keyword"> override</span></div><div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;<span class="keyword">        </span>{</div><div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;            Vecd grad_ij = transf_diffusivity_ * inter_particle_direction;</div><div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;            <span class="keywordflow">return</span> 1.0 / grad_ij.scalarNormSqr();</div><div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;        };</div><div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;    };</div><div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;</div><div class="line"><a name="l00147"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_local_directional_diffusion.html">  147</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_local_directional_diffusion.html">LocalDirectionalDiffusion</a> : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_directional_diffusion.html">DirectionalDiffusion</a></div><div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;    {</div><div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160; 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           Real diff_cf, Real bias_diff_cf, Vecd bias_direction)</div><div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;            : <a class="code" href="class_s_p_h_1_1_directional_diffusion.html">DirectionalDiffusion</a>(diffusion_species_index, gradient_species_index, diff_cf, bias_diff_cf, bias_direction) {};</div><div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_local_directional_diffusion.html">LocalDirectionalDiffusion</a>() {};</div><div class="line"><a name="l00166"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_local_directional_diffusion.html#a3d7732c37df4d03daccbfa489d856998">  166</a></span>&#160;        <span class="keyword">virtual</span> Real <a class="code" href="class_s_p_h_1_1_local_directional_diffusion.html#a3d7732c37df4d03daccbfa489d856998">getInterParticleDiffusionCoff</a>(<span class="keywordtype">size_t</span> particle_index_i, <span class="keywordtype">size_t</span> particle_index_j, Vecd&amp; inter_particle_direction)<span class="keyword"> override</span></div><div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;<span class="keyword">        </span>{</div><div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;            Matd trans_diffusivity = getAverageValue(local_transf_diffusivity_[particle_index_i], local_transf_diffusivity_[particle_index_j]);</div><div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;            Vecd grad_ij = trans_diffusivity * inter_particle_direction;</div><div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;            <span class="keywordflow">return</span> 1.0 / grad_ij.scalarNormSqr();</div><div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;        };</div><div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> initializeLocalDiffusionProperties(<a class="code" href="class_s_p_h_1_1_base_particles.html">BaseParticles</a>* base_particles) <span class="keyword">override</span>;</div><div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160; 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   {</div><div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> assignDerivedReactionParameters() = 0;</div><div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00191"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_base_reaction_model.html#a446811dd226c7f841e6156f27ebf99a6">  191</a></span>&#160;        <a class="code" href="class_s_p_h_1_1_base_reaction_model.html#a446811dd226c7f841e6156f27ebf99a6">BaseReactionModel</a>() {};</div><div class="line"><a name="l00192"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_base_reaction_model.html#a5d7b0f83c36dd9b3efd1c5a8c74f2073">  192</a></span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_base_reaction_model.html">BaseReactionModel</a>() {};</div><div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;</div><div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;        <a class="code" href="namespace_s_p_h.html#abae56fd7f25f13487c7943ce4681d0ce">IndexVector</a> reactive_species_;</div><div class="line"><a name="l00197"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_base_reaction_model.html#a910ab731d18d21e073360a0e837e9dc9">  197</a></span>&#160;        StdVec&lt;ReactionFunctor&gt; <a class="code" href="class_s_p_h_1_1_base_reaction_model.html#a910ab731d18d21e073360a0e837e9dc9">get_production_rates_</a>;</div><div class="line"><a name="l00199"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_base_reaction_model.html#ac9370e5551fc733dccfa12e9364bb27d">  199</a></span>&#160;        StdVec&lt;ReactionFunctor&gt; <a class="code" href="class_s_p_h_1_1_base_reaction_model.html#ac9370e5551fc733dccfa12e9364bb27d">get_loss_rates_</a>;</div><div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;    };</div><div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;</div><div class="line"><a name="l00208"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_electro_physiology_reaction.html">  208</a></span>&#160; 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       <a class="code" href="class_s_p_h_1_1_base_reaction_model.html">BaseReactionModel</a>* <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html#a5e934e496e6bc76cfac9878df8ff36d7">species_reaction_</a>;</div><div class="line"><a name="l00276"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_material.html#ae4f0b595243d37c432706f000aceae57">  276</a></span>&#160;        <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html">DiffusionReactionParticles&lt;BaseParticlesType, BaseMaterialType&gt;</a>* <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html#ae4f0b595243d37c432706f000aceae57">diffusion_reaction_particles_</a>;</div><div class="line"><a name="l00277"></a><span class="lineno">  277</span>&#160;</div><div class="line"><a name="l00279"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_material.html#a79430183ccaea36384dd3d54b89a5160">  279</a></span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html#a79430183ccaea36384dd3d54b89a5160">assignDerivedMaterialParameters</a>()<span class="keyword"> override </span></div><div class="line"><a name="l00280"></a><span class="lineno">  280</span>&#160;<span class="keyword">        </span>{</div><div class="line"><a name="l00281"></a><span class="lineno">  281</span>&#160; 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       };</div><div class="line"><a name="l00292"></a><span class="lineno">  292</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00294"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_material.html#ac3b04fe5b64e8374b18142c63dcadc74">  294</a></span>&#160;        <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html#ac3b04fe5b64e8374b18142c63dcadc74">DiffusionReactionMaterial</a>() </div><div class="line"><a name="l00295"></a><span class="lineno">  295</span>&#160;            : <a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>(), number_of_species_(0), species_reaction_(NULL) </div><div class="line"><a name="l00296"></a><span class="lineno">  296</span>&#160;        {</div><div class="line"><a name="l00297"></a><span class="lineno">  297</span>&#160;            BaseMaterialType::material_name_ = <span class="stringliteral">&quot;DiffusionMaterial&quot;</span>;</div><div class="line"><a name="l00298"></a><span class="lineno">  298</span>&#160;        };</div><div class="line"><a name="l00300"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_material.html#a129c308dd850749a9e8a5161630121f9">  300</a></span>&#160;        <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html#a129c308dd850749a9e8a5161630121f9">DiffusionReactionMaterial</a>(<a class="code" href="class_s_p_h_1_1_base_reaction_model.html">BaseReactionModel</a>* species_reaction)</div><div class="line"><a name="l00301"></a><span class="lineno">  301</span>&#160;            : <a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>(), number_of_species_(0), species_reaction_(species_reaction) </div><div class="line"><a name="l00302"></a><span class="lineno">  302</span>&#160;        {</div><div class="line"><a name="l00303"></a><span class="lineno">  303</span>&#160;            BaseMaterialType::material_name_ = <span class="stringliteral">&quot;DiffusionReactionMaterial&quot;</span>;</div><div class="line"><a name="l00304"></a><span class="lineno">  304</span>&#160;        };</div><div class="line"><a name="l00305"></a><span class="lineno">  305</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html">DiffusionReactionMaterial</a>() {};</div><div class="line"><a name="l00306"></a><span class="lineno">  306</span>&#160;</div><div class="line"><a name="l00308"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_material.html#afa18fb6a34828623808f9496176e20a0">  308</a></span>&#160;        <span class="keywordtype">size_t</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html#afa18fb6a34828623808f9496176e20a0">getNumberOfSpecies</a>() { <span class="keywordflow">return</span> number_of_species_; };</div><div class="line"><a name="l00310"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_material.html#a7d4bb22f601d41db5e573a9355ff200a">  310</a></span>&#160;        StdVec&lt;BaseDiffusion*&gt; <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html#a7d4bb22f601d41db5e573a9355ff200a">getDiffusionSpecies</a>() { <span class="keywordflow">return</span> species_diffusion_; };</div><div class="line"><a name="l00312"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_material.html#a2e1bdfc902c0dcd3a9540ef597e3e6b1">  312</a></span>&#160;        <a class="code" href="class_s_p_h_1_1_base_reaction_model.html">BaseReactionModel</a>* <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html#a2e1bdfc902c0dcd3a9540ef597e3e6b1">getReactionModel</a>() { <span class="keywordflow">return</span> species_reaction_; };</div><div class="line"><a name="l00314"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_material.html#a32436a338edbc5a36c4e062b612db954">  314</a></span>&#160;        <a class="code" href="classmap_3_01string_00_01size__t_01_4.html">map&lt;string, size_t&gt;</a> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html#a32436a338edbc5a36c4e062b612db954">getSpeciesIndexMap</a>() { <span class="keywordflow">return</span>  species_indexes_map_; };</div><div class="line"><a name="l00316"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_material.html#aab5473ccc3ee73b04028b239cd18614c">  316</a></span>&#160; 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       };</div><div class="line"><a name="l00325"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_material.html#a07649784c6535035ad8331c87ec19e30">  325</a></span>&#160;        Real <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html#a07649784c6535035ad8331c87ec19e30">getDiffusionTimeStepSize</a>(Real smoothing_length) </div><div class="line"><a name="l00326"></a><span class="lineno">  326</span>&#160;        {</div><div class="line"><a name="l00327"></a><span class="lineno">  327</span>&#160;            Real diff_coff_max = 0.0;</div><div class="line"><a name="l00328"></a><span class="lineno">  328</span>&#160;            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> k = 0; k &lt; species_diffusion_.size(); ++k)</div><div class="line"><a name="l00329"></a><span class="lineno">  329</span>&#160;                diff_coff_max = SMAX(diff_coff_max, species_diffusion_[k]-&gt;getReferenceDiffusivity());</div><div class="line"><a name="l00330"></a><span class="lineno">  330</span>&#160;            Real dimension = Real(Vecd(0).size());</div><div class="line"><a name="l00331"></a><span class="lineno">  331</span>&#160;            <span class="keywordflow">return</span> 0.5 * smoothing_length * smoothing_length / diff_coff_max / dimension;</div><div class="line"><a name="l00332"></a><span class="lineno">  332</span>&#160;        };</div><div class="line"><a name="l00334"></a><span class="lineno">  334</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> initializeDiffusion() = 0;</div><div class="line"><a name="l00335"></a><span class="lineno">  335</span>&#160;</div><div class="line"><a name="l00337"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_material.html#afc50002a857b8788e490a5862d2ef921">  337</a></span>&#160;        <span class="keyword">virtual</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html">DiffusionReactionMaterial&lt;BaseParticlesType, BaseMaterialType&gt;</a>* <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html#afc50002a857b8788e490a5862d2ef921">PointToThisObject</a>()<span class="keyword"> override </span>{</div><div class="line"><a name="l00338"></a><span class="lineno">  338</span>&#160;            <span class="keywordflow">return</span> <span class="keyword">this</span>;</div><div class="line"><a name="l00339"></a><span class="lineno">  339</span>&#160;        };</div><div class="line"><a name="l00340"></a><span class="lineno">  340</span>&#160;    };</div><div class="line"><a name="l00341"></a><span class="lineno">  341</span>&#160;</div><div class="line"><a name="l00346"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_mono_field_electro_physiology.html">  346</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_mono_field_electro_physiology.html">MonoFieldElectroPhysiology</a> </div><div class="line"><a name="l00347"></a><span class="lineno">  347</span>&#160;        : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html">DiffusionReactionMaterial</a>&lt;SolidParticles, Solid&gt;</div><div class="line"><a name="l00348"></a><span class="lineno">  348</span>&#160;    {</div><div class="line"><a name="l00349"></a><span class="lineno">  349</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00350"></a><span class="lineno">  350</span>&#160;        Real diff_cf_;</div><div class="line"><a name="l00351"></a><span class="lineno">  351</span>&#160;        Real bias_diff_cf_; </div><div class="line"><a name="l00352"></a><span class="lineno">  352</span>&#160;        Vecd bias_direction_;</div><div class="line"><a name="l00353"></a><span class="lineno">  353</span>&#160;</div><div class="line"><a name="l00355"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_mono_field_electro_physiology.html#a3926b5e0471f71195c23f24b4f2a6986">  355</a></span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_mono_field_electro_physiology.html#a3926b5e0471f71195c23f24b4f2a6986">assignDerivedMaterialParameters</a>()<span class="keyword"> override</span></div><div class="line"><a name="l00356"></a><span class="lineno">  356</span>&#160;<span class="keyword">        </span>{</div><div class="line"><a name="l00357"></a><span class="lineno">  357</span>&#160;            <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html">DiffusionReactionMaterial&lt;SolidParticles, Solid&gt;::assignDerivedMaterialParameters</a>();</div><div class="line"><a name="l00358"></a><span class="lineno">  358</span>&#160;        };</div><div class="line"><a name="l00359"></a><span class="lineno">  359</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00361"></a><span class="lineno">  361</span>&#160;        <a class="code" href="class_s_p_h_1_1_mono_field_electro_physiology.html">MonoFieldElectroPhysiology</a>(<a class="code" href="class_s_p_h_1_1_electro_physiology_reaction.html">ElectroPhysiologyReaction</a>* electro_physiology_reaction);</div><div class="line"><a name="l00362"></a><span class="lineno">  362</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_mono_field_electro_physiology.html">MonoFieldElectroPhysiology</a>() {};</div><div class="line"><a name="l00363"></a><span class="lineno">  363</span>&#160;</div><div class="line"><a name="l00365"></a><span class="lineno">  365</span>&#160; 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       };</div><div class="line"><a name="l00403"></a><span class="lineno">  403</span>&#160;    };</div><div class="line"><a name="l00404"></a><span class="lineno">  404</span>&#160;}</div><div class="ttc" id="class_s_p_h_1_1_base_diffusion_html"><div class="ttname"><a href="class_s_p_h_1_1_base_diffusion.html">SPH::BaseDiffusion</a></div><div class="ttdoc">diffusion property abstract base class. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:51</div></div>
<div class="ttc" id="namespace_s_p_h_html_ae3b5e80e4c20e54eefb0956471f5c2c0"><div class="ttname"><a href="namespace_s_p_h.html#ae3b5e80e4c20e54eefb0956471f5c2c0">SPH::ReactionFunctor</a></div><div class="ttdeci">std::function&lt; Real(StdVec&lt; Real &gt; &amp;)&gt; ReactionFunctor</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:179</div></div>
<div class="ttc" id="namespacestd_1_1placeholders_html"><div class="ttname"><a href="namespacestd_1_1placeholders.html">placeholders</a></div></div>
<div class="ttc" id="class_s_p_h_1_1_isotropic_diffusion_html"><div class="ttname"><a href="class_s_p_h_1_1_isotropic_diffusion.html">SPH::IsotropicDiffusion</a></div><div class="ttdoc">isotropic diffusion property. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:78</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html_a7d4bb22f601d41db5e573a9355ff200a"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#a7d4bb22f601d41db5e573a9355ff200a">SPH::DiffusionReactionMaterial::getDiffusionSpecies</a></div><div class="ttdeci">StdVec&lt; BaseDiffusion * &gt; getDiffusionSpecies()</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:310</div></div>
<div class="ttc" id="class_s_p_h_1_1_local_mono_field_electro_physiology_html_a48282f42985434fa051660d48f3c1b2a"><div class="ttname"><a href="class_s_p_h_1_1_local_mono_field_electro_physiology.html#a48282f42985434fa051660d48f3c1b2a">SPH::LocalMonoFieldElectroPhysiology::LocalMonoFieldElectroPhysiology</a></div><div class="ttdeci">LocalMonoFieldElectroPhysiology(ElectroPhysiologyReaction *electro_physiology_reaction)</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:389</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_particles_html"><div class="ttname"><a href="class_s_p_h_1_1_base_particles.html">SPH::BaseParticles</a></div><div class="ttdoc">Particles with essential (geometric and kinematic) data. There are three types of particles...</div><div class="ttdef"><b>Definition:</b> base_particles.h:87</div></div>
<div class="ttc" id="class_s_p_h_1_1_directional_diffusion_html_a9cddff8508ce415c43e169d522e3e1d8"><div class="ttname"><a href="class_s_p_h_1_1_directional_diffusion.html#a9cddff8508ce415c43e169d522e3e1d8">SPH::DirectionalDiffusion::getInterParticleDiffusionCoff</a></div><div class="ttdeci">virtual Real getInterParticleDiffusionCoff(size_t particle_index_i, size_t particle_index_j, Vecd &amp;inter_particle_direction) override</div><div class="ttdoc">Obtain diffusion coefficient along the interacting particle direction. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:136</div></div>
<div class="ttc" id="class_s_p_h_1_1_isotropic_diffusion_html_aac18dd1f017b84629c0f283f91aeaa3d"><div class="ttname"><a href="class_s_p_h_1_1_isotropic_diffusion.html#aac18dd1f017b84629c0f283f91aeaa3d">SPH::IsotropicDiffusion::getInterParticleDiffusionCoff</a></div><div class="ttdeci">virtual Real getInterParticleDiffusionCoff(size_t particle_i, size_t particle_j, Vecd &amp;direction_from_j_to_i) override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:93</div></div>
<div class="ttc" id="class_s_p_h_1_1_directional_diffusion_html_a105351f84960ad51e5d47cf3a1ddb2e4"><div class="ttname"><a href="class_s_p_h_1_1_directional_diffusion.html#a105351f84960ad51e5d47cf3a1ddb2e4">SPH::DirectionalDiffusion::getReferenceDiffusivity</a></div><div class="ttdeci">virtual Real getReferenceDiffusivity() override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:126</div></div>
<div class="ttc" id="namespace_s_p_h_html_abae56fd7f25f13487c7943ce4681d0ce"><div class="ttname"><a href="namespace_s_p_h.html#abae56fd7f25f13487c7943ce4681d0ce">SPH::IndexVector</a></div><div class="ttdeci">StdVec&lt; size_t &gt; IndexVector</div><div class="ttdef"><b>Definition:</b> sph_data_conainers.h:30</div></div>
<div class="ttc" id="class_s_p_h_1_1_mono_field_electro_physiology_html_a3926b5e0471f71195c23f24b4f2a6986"><div class="ttname"><a href="class_s_p_h_1_1_mono_field_electro_physiology.html#a3926b5e0471f71195c23f24b4f2a6986">SPH::MonoFieldElectroPhysiology::assignDerivedMaterialParameters</a></div><div class="ttdeci">virtual void assignDerivedMaterialParameters() override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:355</div></div>
<div class="ttc" id="class_s_p_h_1_1_directional_diffusion_html"><div class="ttname"><a href="class_s_p_h_1_1_directional_diffusion.html">SPH::DirectionalDiffusion</a></div><div class="ttdoc">Diffussion is biased along a specific direction. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:103</div></div>
<div class="ttc" id="class_s_p_h_1_1_directional_diffusion_html_ac02518b789d53ccf663d037b16a1a0d5"><div class="ttname"><a href="class_s_p_h_1_1_directional_diffusion.html#ac02518b789d53ccf663d037b16a1a0d5">SPH::DirectionalDiffusion::DirectionalDiffusion</a></div><div class="ttdeci">DirectionalDiffusion(size_t diffusion_species_index, size_t gradient_species_index, Real diff_cf, Real bias_diff_cf, Vecd bias_direction)</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:115</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html_a07649784c6535035ad8331c87ec19e30"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#a07649784c6535035ad8331c87ec19e30">SPH::DiffusionReactionMaterial::getDiffusionTimeStepSize</a></div><div class="ttdeci">Real getDiffusionTimeStepSize(Real smoothing_length)</div><div class="ttdoc">Get diffusion time step size. Here, I follow the reference: https://www.uni-muenster.de/imperia/md/content/physik_tp/lectures/ws2016-2017/num_methods_i/heat.pdf. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:325</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_reaction_model_html_ac9370e5551fc733dccfa12e9364bb27d"><div class="ttname"><a href="class_s_p_h_1_1_base_reaction_model.html#ac9370e5551fc733dccfa12e9364bb27d">SPH::BaseReactionModel::get_loss_rates_</a></div><div class="ttdeci">StdVec&lt; ReactionFunctor &gt; get_loss_rates_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:199</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html_a129c308dd850749a9e8a5161630121f9"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#a129c308dd850749a9e8a5161630121f9">SPH::DiffusionReactionMaterial::DiffusionReactionMaterial</a></div><div class="ttdeci">DiffusionReactionMaterial(BaseReactionModel *species_reaction)</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:300</div></div>
<div class="ttc" id="class_s_p_h_1_1_aliev_panfilow_model_html"><div class="ttname"><a href="class_s_p_h_1_1_aliev_panfilow_model.html">SPH::AlievPanfilowModel</a></div><div class="ttdoc">The simplest Electrophysiology Reaction model, which reduces the complex of array of ion currents to ...</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:235</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html_ac3b04fe5b64e8374b18142c63dcadc74"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#ac3b04fe5b64e8374b18142c63dcadc74">SPH::DiffusionReactionMaterial::DiffusionReactionMaterial</a></div><div class="ttdeci">DiffusionReactionMaterial()</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:294</div></div>
<div class="ttc" id="class_s_p_h_1_1_mono_field_electro_physiology_html"><div class="ttname"><a href="class_s_p_h_1_1_mono_field_electro_physiology.html">SPH::MonoFieldElectroPhysiology</a></div><div class="ttdoc">material class for electro_physiology. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:346</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html_ae4f0b595243d37c432706f000aceae57"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#ae4f0b595243d37c432706f000aceae57">SPH::DiffusionReactionMaterial::diffusion_reaction_particles_</a></div><div class="ttdeci">DiffusionReactionParticles&lt; BaseParticlesType, BaseMaterialType &gt; * diffusion_reaction_particles_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:276</div></div>
<div class="ttc" id="class_s_p_h_1_1_local_directional_diffusion_html_ab3664aef5c5897af2a5b11381f2b9563"><div class="ttname"><a href="class_s_p_h_1_1_local_directional_diffusion.html#ab3664aef5c5897af2a5b11381f2b9563">SPH::LocalDirectionalDiffusion::LocalDirectionalDiffusion</a></div><div class="ttdeci">LocalDirectionalDiffusion(size_t diffusion_species_index, size_t gradient_species_index, Real diff_cf, Real bias_diff_cf, Vecd bias_direction)</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:156</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_reaction_model_html_a910ab731d18d21e073360a0e837e9dc9"><div class="ttname"><a href="class_s_p_h_1_1_base_reaction_model.html#a910ab731d18d21e073360a0e837e9dc9">SPH::BaseReactionModel::get_production_rates_</a></div><div class="ttdeci">StdVec&lt; ReactionFunctor &gt; get_production_rates_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:197</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html">SPH::DiffusionReactionMaterial</a></div><div class="ttdoc">Complex material for diffusion or/and reactions. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:263</div></div>
<div class="ttc" id="class_s_p_h_1_1_local_mono_field_electro_physiology_html"><div class="ttname"><a href="class_s_p_h_1_1_local_mono_field_electro_physiology.html">SPH::LocalMonoFieldElectroPhysiology</a></div><div class="ttdoc">material class for electro_physiology with locally oriented fibers. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:378</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_diffusion_html_a4d54baaebbd670cd125cfc2874a2b6ff"><div class="ttname"><a href="class_s_p_h_1_1_base_diffusion.html#a4d54baaebbd670cd125cfc2874a2b6ff">SPH::BaseDiffusion::setupLocalDiffusionProperties</a></div><div class="ttdeci">virtual void setupLocalDiffusionProperties(StdVec&lt; Vecd &gt; &amp;material_fiber)</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:71</div></div>
<div class="ttc" id="class_s_p_h_1_1_electro_physiology_particles_html"><div class="ttname"><a href="class_s_p_h_1_1_electro_physiology_particles.html">SPH::ElectroPhysiologyParticles</a></div><div class="ttdoc">A group of particles with electrophysiology particle data. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:186</div></div>
<div class="ttc" id="class_s_p_h_1_1_electro_physiology_reaction_html"><div class="ttname"><a href="class_s_p_h_1_1_electro_physiology_reaction.html">SPH::ElectroPhysiologyReaction</a></div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:208</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html_a79430183ccaea36384dd3d54b89a5160"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#a79430183ccaea36384dd3d54b89a5160">SPH::DiffusionReactionMaterial::assignDerivedMaterialParameters</a></div><div class="ttdeci">virtual void assignDerivedMaterialParameters() override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:279</div></div>
<div class="ttc" id="class_s_p_h_1_1_local_mono_field_electro_physiology_html_af0d32cb1324fc692264a3014d69c2384"><div class="ttname"><a href="class_s_p_h_1_1_local_mono_field_electro_physiology.html#af0d32cb1324fc692264a3014d69c2384">SPH::LocalMonoFieldElectroPhysiology::assignDerivedMaterialParameters</a></div><div class="ttdeci">virtual void assignDerivedMaterialParameters() override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:383</div></div>
<div class="ttc" id="classmap_3_01string_00_01size__t_01_4_html"><div class="ttname"><a href="classmap_3_01string_00_01size__t_01_4.html">map&lt; string, size_t &gt;</a></div></div>
<div class="ttc" id="base__material_8h_html"><div class="ttname"><a href="base__material_8h.html">base_material.h</a></div><div class="ttdoc">This is the base classes of all materials. A function in a derived material class returns a value wit...</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html_a32436a338edbc5a36c4e062b612db954"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#a32436a338edbc5a36c4e062b612db954">SPH::DiffusionReactionMaterial::getSpeciesIndexMap</a></div><div class="ttdeci">map&lt; string, size_t &gt; getSpeciesIndexMap()</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:314</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html_aab5473ccc3ee73b04028b239cd18614c"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#aab5473ccc3ee73b04028b239cd18614c">SPH::DiffusionReactionMaterial::assignDiffusionReactionParticles</a></div><div class="ttdeci">void assignDiffusionReactionParticles(DiffusionReactionParticles&lt; BaseParticlesType, BaseMaterialType &gt; *diffusion_reaction_particles)</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:316</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html_a5e934e496e6bc76cfac9878df8ff36d7"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#a5e934e496e6bc76cfac9878df8ff36d7">SPH::DiffusionReactionMaterial::species_reaction_</a></div><div class="ttdeci">BaseReactionModel * species_reaction_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:274</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html_afa18fb6a34828623808f9496176e20a0"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#afa18fb6a34828623808f9496176e20a0">SPH::DiffusionReactionMaterial::getNumberOfSpecies</a></div><div class="ttdeci">size_t getNumberOfSpecies()</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:308</div></div>
<div class="ttc" id="class_s_p_h_1_1_local_mono_field_electro_physiology_html_a2f2d7945024607f7799da32d160f6357"><div class="ttname"><a href="class_s_p_h_1_1_local_mono_field_electro_physiology.html#a2f2d7945024607f7799da32d160f6357">SPH::LocalMonoFieldElectroPhysiology::PointToThisObject</a></div><div class="ttdeci">virtual LocalMonoFieldElectroPhysiology * PointToThisObject() override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:399</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_reaction_model_html"><div class="ttname"><a href="class_s_p_h_1_1_base_reaction_model.html">SPH::BaseReactionModel</a></div><div class="ttdoc">Base class for all reaction models. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:184</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html_afe0d1dcde9013eaa58c221c03396f8f7"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#afe0d1dcde9013eaa58c221c03396f8f7">SPH::DiffusionReactionMaterial::species_diffusion_</a></div><div class="ttdeci">StdVec&lt; BaseDiffusion * &gt; species_diffusion_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:272</div></div>
<div class="ttc" id="class_s_p_h_1_1_local_directional_diffusion_html"><div class="ttname"><a href="class_s_p_h_1_1_local_directional_diffusion.html">SPH::LocalDirectionalDiffusion</a></div><div class="ttdoc">Diffusion is biased along a specific direction. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:147</div></div>
<div class="ttc" id="class_s_p_h_1_1_electro_physiology_reaction_html_af4a599128cbbe5686115f6cd86432104"><div class="ttname"><a href="class_s_p_h_1_1_electro_physiology_reaction.html#af4a599128cbbe5686115f6cd86432104">SPH::ElectroPhysiologyReaction::assignDerivedReactionParameters</a></div><div class="ttdeci">virtual void assignDerivedReactionParameters() override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:225</div></div>
<div class="ttc" id="class_s_p_h_1_1_isotropic_diffusion_html_a8778717ace62181005a763fed4ce3f8c"><div class="ttname"><a href="class_s_p_h_1_1_isotropic_diffusion.html#a8778717ace62181005a763fed4ce3f8c">SPH::IsotropicDiffusion::getReferenceDiffusivity</a></div><div class="ttdeci">virtual Real getReferenceDiffusivity() override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:91</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html_a905a29d5dad718e0fc2ad51a358979b3"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#a905a29d5dad718e0fc2ad51a358979b3">SPH::DiffusionReactionMaterial::species_indexes_map_</a></div><div class="ttdeci">map&lt; string, size_t &gt; species_indexes_map_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:270</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_material_type_html"><div class="ttname"><a href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a></div></div>
<div class="ttc" id="class_s_p_h_1_1_aliev_panfilow_model_html_a93a96d67615c5cb5bc3d7e1cc8a7f54e"><div class="ttname"><a href="class_s_p_h_1_1_aliev_panfilow_model.html#a93a96d67615c5cb5bc3d7e1cc8a7f54e">SPH::AlievPanfilowModel::assignDerivedReactionParameters</a></div><div class="ttdeci">virtual void assignDerivedReactionParameters() override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:247</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_particles_html"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html">SPH::DiffusionReactionParticles</a></div><div class="ttdoc">A group of particles with diffusion or/and reactions particle data. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:45</div></div>
<div class="ttc" id="class_std_vec_3_01_real_01_4_html"><div class="ttname"><a href="class_std_vec_3_01_real_01_4.html">StdVec&lt; Real &gt;</a></div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html_a6c6417797c31d67fd80264feed5134cf"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#a6c6417797c31d67fd80264feed5134cf">SPH::DiffusionReactionMaterial::number_of_species_</a></div><div class="ttdeci">size_t number_of_species_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:268</div></div>
<div class="ttc" id="class_s_p_h_1_1_isotropic_diffusion_html_a747fa5685c40065bf66e758301ffe5de"><div class="ttname"><a href="class_s_p_h_1_1_isotropic_diffusion.html#a747fa5685c40065bf66e758301ffe5de">SPH::IsotropicDiffusion::IsotropicDiffusion</a></div><div class="ttdeci">IsotropicDiffusion(size_t diffusion_species_index, size_t gradient_species_index, Real diff_cf=1.0)</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:85</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html_a2e1bdfc902c0dcd3a9540ef597e3e6b1"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#a2e1bdfc902c0dcd3a9540ef597e3e6b1">SPH::DiffusionReactionMaterial::getReactionModel</a></div><div class="ttdeci">BaseReactionModel * getReactionModel()</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:312</div></div>
<div class="ttc" id="solid__particles_8h_html"><div class="ttname"><a href="solid__particles_8h.html">solid_particles.h</a></div><div class="ttdoc">This is the derived class of base particle. </div></div>
<div class="ttc" id="class_s_p_h_1_1_local_directional_diffusion_html_a3d7732c37df4d03daccbfa489d856998"><div class="ttname"><a href="class_s_p_h_1_1_local_directional_diffusion.html#a3d7732c37df4d03daccbfa489d856998">SPH::LocalDirectionalDiffusion::getInterParticleDiffusionCoff</a></div><div class="ttdeci">virtual Real getInterParticleDiffusionCoff(size_t particle_index_i, size_t particle_index_j, Vecd &amp;inter_particle_direction) override</div><div class="ttdoc">Obtain diffusion coefficient along the interacting particle direction. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:166</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_reaction_model_html_a446811dd226c7f841e6156f27ebf99a6"><div class="ttname"><a href="class_s_p_h_1_1_base_reaction_model.html#a446811dd226c7f841e6156f27ebf99a6">SPH::BaseReactionModel::BaseReactionModel</a></div><div class="ttdeci">BaseReactionModel()</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:191</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_diffusion_html_a1b83eb4cf023bf6fc5249f51b856494b"><div class="ttname"><a href="class_s_p_h_1_1_base_diffusion.html#a1b83eb4cf023bf6fc5249f51b856494b">SPH::BaseDiffusion::gradient_species_index_</a></div><div class="ttdeci">size_t gradient_species_index_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:62</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html_afc50002a857b8788e490a5862d2ef921"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#afc50002a857b8788e490a5862d2ef921">SPH::DiffusionReactionMaterial::PointToThisObject</a></div><div class="ttdeci">virtual DiffusionReactionMaterial&lt; BaseParticlesType, BaseMaterialType &gt; * PointToThisObject() override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:337</div></div>
<div class="ttc" id="class_s_p_h_1_1_mono_field_electro_physiology_html_a542d07690fbe8495be5e919bf9db9d2d"><div class="ttname"><a href="class_s_p_h_1_1_mono_field_electro_physiology.html#a542d07690fbe8495be5e919bf9db9d2d">SPH::MonoFieldElectroPhysiology::PointToThisObject</a></div><div class="ttdeci">virtual MonoFieldElectroPhysiology * PointToThisObject() override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:368</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_diffusion_html_ad0641c7cb654e35b59e3ffc15472b9a1"><div class="ttname"><a href="class_s_p_h_1_1_base_diffusion.html#ad0641c7cb654e35b59e3ffc15472b9a1">SPH::BaseDiffusion::initializeLocalDiffusionProperties</a></div><div class="ttdeci">virtual void initializeLocalDiffusionProperties(BaseParticles *base_particles)</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:69</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html_a3af74807ed8e3f8cafd9fd3190760ea0"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#a3af74807ed8e3f8cafd9fd3190760ea0">SPH::DiffusionReactionMaterial::insertASpecies</a></div><div class="ttdeci">void insertASpecies(string species_name)</div><div class="ttdoc">Insert a species. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:287</div></div>
<div class="ttc" id="namespace_s_p_h_html"><div class="ttname"><a href="namespace_s_p_h.html">SPH</a></div><div class="ttdef"><b>Definition:</b> base_body_supplementary.cpp:11</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_diffusion_html_ad28fcfc65a19319a7ee1480e4e5ba9a6"><div class="ttname"><a href="class_s_p_h_1_1_base_diffusion.html#ad28fcfc65a19319a7ee1480e4e5ba9a6">SPH::BaseDiffusion::BaseDiffusion</a></div><div class="ttdeci">BaseDiffusion(size_t diffusion_species_index, size_t gradient_species_index)</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:55</div></div>
<div class="ttc" id="class_s_p_h_1_1_aliev_panfilow_model_html_ac926a3fcc24e3f7b65e2d87fa59662b4"><div class="ttname"><a href="class_s_p_h_1_1_aliev_panfilow_model.html#ac926a3fcc24e3f7b65e2d87fa59662b4">SPH::AlievPanfilowModel::k_</a></div><div class="ttdeci">Real k_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:239</div></div>
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